Package edu.msu.cme.rdp.classifier.train.validation.distance

Class TaxaSimilarityMain

java.lang.Object
edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
public class TaxaSimilarityMain extends Object

  • Field Details

    • RANKS

      public static String[] RANKS

  • Constructor Details

    • TaxaSimilarityMain

      public TaxaSimilarityMain(List<String> selectedRanks)

  • Method Details

    • readRanks

      public static List<String> readRanks(String rankFile) throws IOException
      Throws:
      IOException

    • getAncestorNodes

      public HashMap<String,HierarchyTree> getAncestorNodes(HierarchyTree root, String seqName, List<String> ancestors)

    • calSabSimilarity

      public void calSabSimilarity(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException
      Throws:
      IOException

    • calPairwiseSimilaritye

      public void calPairwiseSimilaritye(String taxonFile, String trainSeqFile, String testSeqFile) throws IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
      Throws:
      IOException
      edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException

    • createPlot

      public void createPlot(String plotTitle, File outdir) throws IOException
      Throws:
      IOException

    • main

      public static void main(String[] args) throws IOException, edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException
      This calculates the average similarity (Sab score or pairwise alignment) between taxa at given ranks and plot the box and whisker plot and accumulation curve. The distances associate to a given rank contains the distances between different child taxa. It does not include the distances within the same child taxa. For example, if a query and it's closest match are from the same genus, the distance value is added to that genus. If there are from different genera but the same family, the distance value is added to that family, etc.
      Parameters:
      args -
      Throws:
      IOException
      edu.msu.cme.rdp.alignment.pairwise.rna.OverlapCheckFailedException